Does anyone have a permanent fix for the trim box on a zxi 900, that keeps taking water in? I understand that they are known for this, but has anyone come up with a seal or fix?

Yes, there is a permanent fix for that.
Order a Kawi P/N 49016-3702 which is a small rubber boot - cheap $3. Install that at the end of of the trim cable at the pump side where there is an exisit rubber boot (smaller than the new one). DO NOT remove the existing boot. The new boot has a large ID end and a small ID end. The large ID end of new boot goes over the existing boot. Zip-tie the both ends of the new boot and the problem is solved.

Trim boot

Look at any oe site that sells kawa parts and you can find it under the 1998 kawa 1100zxi. Below is where I buy my parts. The kawa oe part number is 49016-3702. Costs 2.18 plus shipping. Use two zip ties to secure.

Now, they will charge about 16.00 to ship so if it were me, I would go to a local dealer and tell them you want to order the part. It will be a lot cheaper overall. AND IT WORKS. I put it on my 1996 kawa 750zxi and my 1998 kawa 100zxi.